The field of synthetic biology has been simmering for quite a while. It occasionally takes a big leap, such as when Venter’s team published about their work on M. genitalium, and it took a big leap recently with the paper about modeling a lot of the cellular processes in a simple cell that I talked [...]
My twitter feed exploded over the last few days with conflama around the new publication about the simulation of the biological processes in a cell. Most of the ire was aimed at a fawning NYT piece that hyped the paper. And yes–the newspaper article is flawed; Jonathan Eisen spoke to that, and then filleted it [...]
BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. [...]
Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment… This is not a bad idea. Boston Sci-Geek Tours. I used to work for the Park [...]
We were on the road last week doing workshops, so this is a few days old now. But if you aren’t on the GO Friends mailing list it’s possible it’s new for you. A quick word about GO Friends list: because so many tools rely on Gene Ontology and have some kind of GO components, [...]
Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment… MetNetMaker: a software tool for making Metabolic Network and pathway representations. [Mary] Genome Workbench v2.1.1 release [...]
Just got an announcement from the Cytoscape mailing list. One of my favorite tutorials* that we’ve developed was Cytoscape–It was an interesting challenge for us because most of our focus has been tools with web interfaces and we had to address installation with this one. But it was such a nice tool with great features [...]
Recently while watching the #bioinformatics tag on Twitter I saw Khader Shameer mention Caleydo. I was instantly hooked at the very clever visualization strategy that they are using to provide more surface area for examining the data you are interested in viewing. Their specific topics are pathways and gene expression, but it got me thinking [...]
Reactome has long been one of our favorite resources for looking at pathways and interactions. The data quality is very high, and there are some very fun tools to use. In fact, they were one of the earliest tutorials we did years back (but of course we have updated since). If you aren’t already familiar [...]
At the Biocuration meeting that I attended back in April, Jim Ostell of NCBI announced that they would soon be releasing a new resource on biological networks. A few weeks ago a friend alerted me that NCBI had released their new BioSystems resource (thanks for the heads-up, Cyndy!) BioSystems is a cool resource that take [...]
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